dealing with homopolymer/low complexity errors

[The_Roads]

Hi,

i am looking through our first pgm run sequencing long pcr fragments and assembling against a ref seq.

we have previously done the same thing on hiseqs with no issues.

for the pgm data we are getting what look like homopolymer seq errors coming through as the majority sequence in specific parts of our assemblies. however we do not know the true extent of these errors.

has anyone got any bioinformatic approaches to deal with of filter these putative errors without running more sequencing?

cheers,
The_Roads